pepflip werkt ook weer

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@344 a1961a4f-ab94-4bcc-80e8-33b5a54de466

src/Secondary.cpp

@@ -820,19 +820,12 @@ DSSPImpl::DSSPImpl(const Structure& s)
 		0.0, [](double s, auto& p) { return s + p.size(); });
 		0.0, [](double s, auto& p) { return s + p.size(); });
 	
 	
 	mResidues.reserve(nRes);
 	mResidues.reserve(nRes);
-
-cerr << "starting to copy atoms for DSSP" << endl;
-auto start = std::chrono::system_clock::now();
 	
 	
 	for (auto& p: mPolymers)
 	for (auto& p: mPolymers)
 	{
 	{
 		for (auto& m: p)
 		for (auto& m: p)
 			mResidues.emplace_back(m);
 			mResidues.emplace_back(m);
 	}
 	}
-
-auto end = std::chrono::system_clock::now();
-chrono::duration<double> diff = end - start;
-cerr << "Copying atoms took " << diff << " seconds" << endl;
 	
 	
 	for (size_t i = 0; i + 1 < mResidues.size(); ++i)
 	for (size_t i = 0; i + 1 < mResidues.size(); ++i)
 	{
 	{

src/Structure.cpp

@@ -1260,7 +1260,6 @@ Structure::Structure(File& f, uint32 modelNr)
 //	sort(mAtoms.begin(), mAtoms.end(), [](auto& a, auto& b) { return a.id() < b.id(); });
 //	sort(mAtoms.begin(), mAtoms.end(), [](auto& a, auto& b) { return a.id() < b.id(); });
 
 
 	// polymers
 	// polymers
-
 	auto& polySeqScheme = category("pdbx_poly_seq_scheme");
 	auto& polySeqScheme = category("pdbx_poly_seq_scheme");
 	
 	
 	for (auto& r: polySeqScheme)
 	for (auto& r: polySeqScheme)
@@ -1273,15 +1272,26 @@ Structure::Structure(File& f, uint32 modelNr)
 			mPolymers.emplace_back(*this, entityID, asymID);
 			mPolymers.emplace_back(*this, entityID, asymID);
 	}
 	}
 }
 }
+
+Structure::Structure(const Structure& s)
+	: mFile(s.mFile), mModelNr(s.mModelNr)
+{
+	mAtoms.reserve(s.mAtoms.size());
+	for (auto& atom: s.mAtoms)
+		mAtoms.emplace_back(atom.clone());
+
+	auto& polySeqScheme = category("pdbx_poly_seq_scheme");
 	
 	
-//	Structure(const Structure& s)
-//		: mFile(s.mFile), mModelNr(s.mModelNr)
-//	{
-//		mAtoms.reserve(si.mAtoms.size());
-//		for (auto& atom: si.mAtoms)
-//			mAtoms.emplace_back(atom.clone());
-//	}
-//}
+	for (auto& r: polySeqScheme)
+	{
+		string asymID, entityID, seqID, monID;
+		cif::tie(asymID, entityID, seqID, monID) =
+			r.get("asym_id", "entity_id", "seq_id", "mon_id");
+		
+		if (mPolymers.empty() or mPolymers.back().asymID() != asymID or mPolymers.back().entityID() != entityID)
+			mPolymers.emplace_back(*this, entityID, asymID);
+	}
+}
 
 
 Structure::~Structure()
 Structure::~Structure()
 {
 {
@@ -1323,21 +1333,6 @@ AtomView Structure::waters() const
 
 
 const list<Polymer>& Structure::polymers() const
 const list<Polymer>& Structure::polymers() const
 {
 {
-//	vector<Polymer> result;
-//	
-//	auto& polySeqScheme = category("pdbx_poly_seq_scheme");
-//	
-//	for (auto& r: polySeqScheme)
-//	{
-//		string asymID, entityID, seqID, monID;
-//		cif::tie(asymID, entityID, seqID, monID) =
-//			r.get("asym_id", "entity_id", "seq_id", "mon_id");
-//		
-//		if (result.empty() or result.back().asymID() != asymID or result.back().entityID() != entityID)
-//			result.emplace_back(*this, entityID, asymID);
-//	}
-//	
-//	return result;
 	return mPolymers;
 	return mPolymers;
 }
 }